Comprehensive Assessment of the Relationship Between Site−2 Specificity and Helix α2 in the Erbin PDZ Domain

PDZ domains are key players in signalling pathways. These modular domains generally recognize short linear C-terminal stretches of sequences in proteins that organize the formation of complex multi-component assemblies. The development of new methodologies for the characterization of the molecular principles governing these interactions is critical to fully understand the functional diversity of the family and to elucidate biological functions for family members. Here, we applied an in vitro evolution strategy to explore comprehensively the capacity of PDZ domains for specific recognition of different amino acids at a key position in C-terminal peptide ligands. We constructed a phage-displayed library of the Erbin PDZ domain by randomizing the binding site⁻² and adjacent residues, which are all contained in helix α2, and we selected for variants binding to a panel of peptides representing all possible position⁻² residues. This approach generated insights into the basis for the common natural class I and II specificities, demonstrated an alternative basis for a rare natural class III specificity for Asp⁻², and revealed a novel specificity for Arg⁻² that has not been reported in natural PDZ domains. A structure of a PDZ-peptide complex explained the minimum requirement for switching specificity from class I ligands containing Thr/Ser⁻² to class II ligands containing hydrophobic residues at position⁻². A second structure explained the molecular basis for the specificity for ligands containing Arg⁻². Overall, the evolved PDZ variants greatly expand our understanding of site⁻² specificities and the variants themselves may prove useful as building blocks for synthetic biology.     

A growing family of Notch ligands

Signaling through Notch-like receptors is an evolutionarily well-conserved mechanism for cell-cell communication. Transmembrane ligands of the DSL (Delta, Serrate, LAG-2) family signal to Notch receptors on a neighboring cell, which results in an intracellular signaling cascade, influencing cellular differentiation. Recently published data shed new light on the repertoire of ligands and on processing of Notch receptors. One report provides evidence for a novel, more distantly related ligand of the Delta-type in mouse, Dll3 (Delta-like 3)¹. Ectopic expression of Dll3 perturbs primary neurogenesis in frog embryos in a manner expected for a bona fide Notch ligand. Two reports provide new information about processing of Notch receptors. A novel protease, Kuzbanian, is identified, which cleaves the Notch receptor at the extracellular side². Biochemical experiments show that the cleavage probably occurs during intracellular trafficking, and that only processed Notch receptors appear at the cell surface³. Taken together, these reports extend our knowledge about an important event in cell-cell communication—how Notch ligands and receptors meet and interact. BioEssays 20:103–107, 1998. © 1998 John Wiley & Sons, Inc.     

Evaluation of two new bifunctional chelates for radiolabeling a parathyroid-specific monoclonal antibody with In-111

BB5-G1, a monoclonal antibody specific for human parathyroid cell membrane antigen was conjugated with two new ligands, BrMe₂HBED and BrφHBED and radiolabeled with ¹¹¹In. We have compared the biodistribution of ¹¹¹In-labeled BBS using the new ligands to conventionally labeled (¹²⁵I-labeled and ¹¹¹In-DTPA-labeled) BBS in a nude mouse model. Both ¹¹¹In-BrMe₂HBED-BB5 and ¹¹¹In-BrφHBED-BB5 attained high parathyroid-to-blood and parathyroid-to-muscle ratios by 72–96 h. ¹¹¹In-BrφHBED-BB5 showed lower %ID/g than ¹¹¹In-BrMe₂HBED-BB5 in the clearance organs, the liver and kidney; renal activity had cleared significantly by 120 h. This work suggests that ¹¹¹In-BrφHBED-BB5 offers improved in vivo behavior and may be useful as a radiopharmaceutical for localizing parathyroid tissue.     

PET radioligands for dopamine receptors and re-uptake sites: Chemistry and biochemistry

This report, based on the past experience of European centres, offers practical guidance on the chemistry and biochemistry of PET radioligands used for the in vivo imaging of dopamine receptors and re-uptake sites. It mainly summarizes methods for the preparation of D1 and D2 receptor ligands labelled with positron-emitting radioisotopes. Some of these ligands (¹¹C-labelled SCH23390, raclopride and nomifensine, ¹⁸F-labelled butyrophenones, [⁷⁶Br]bromolisuride), which have been found useful in PET clinical investigations, have been emphasized. This report is intended as an introduction and guideline for new PET-groups who want to start research in the dopaminergic neurotransmission imaging field.     

Ligand Pose and Orientational Sampling in Molecular Docking

Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×10¹⁰ to 4×10¹⁰ to 1×10¹¹ to 2×10¹¹ to 5×10¹¹ mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.     

N-methyl-bis(2-bromo 6-pyridylmethyl)amine: high yield synthesis, and spectroscopic properties of the dichloroferrous complex with trigonal bipyramidal geometry

The new tridentate title ligand has been synthesized by a very convenient and high yield method. The dichloroferrous derivative was prepared in order to provide spectroscopic bases for solution studies of trigonal bipyramidal derivatives with aminomethylpyridyl containing ligands. Its crystal structure is reported, together with UV-Vis, ¹H NMR and molecular conductivity data. The absence of any MLCT in UV-Vis, significant broadening of the β and β′ resonances in ¹H NMR and neutral electrolytic behavior are reported and taken together, these parameters can now unequivocally serve as criteria to detect any tridentate coordination mode of the tripod in the chemistry of dichloroferrous complexes with tris-(2-pyridylmethyl)amine type ligands.     

Development of a sensitive method for selection of affinity ligand for trypsin using quartz crystal microbalance sensor

In this work, a new methodology is developed for selection of affinity ligands towards the enzyme “trypsin” using quartz crystals microbalance (QCM) technique. To achieve this goal, the surface amination of gold plated QCM crystals was achieved in 13.56 MHz plasma polymerization system by using ethylenediamine. Three different ligands (i.e., 4-aminobenzamidine, 4-aminobenzoic acid, and phenylalanine) were immobilized on the aminated QCM crystals surface via glutaraldhyde coupling. All three ligand immobilized QCM crystals were characterized and compared under different experimental conditions. It was observed that the benzamidine ligand showed higher affinity to trypsin with a dissociation constant on the order of 1.76 × 10⁻⁹ M, which is within the range of 10⁻⁴–10⁻⁸ M for affinity ligands. Thus, its selectivity was suitable for purification of trypsin from biological fluids.     

Exploring computational lead optimisation with affinity constants obtained by surface plasmon resonance for the interaction of PorA epitope peptides with antibody against Neisseria meningitidis

LUDI is a program used for de novo structure-based design of ligands and can predict binding of ligands quantitatively using a scoring function. Here we evaluate LUDI in a lead optimisation study with ligands for the antibody MN12H2, that has been raised against outer membrane protein PorA epitope P1.16 of Neisseria meningitidis. The ligands were synthetic peptides that are derived from the smallest binding epitope ¹⁸²DTNNN¹⁸⁶. LUDI’s fragment building rules are used for the proposal of new peptide-ligands for MN12H2 and were focused on replacements of Asp¹⁸⁶ in the epitope. Accordingly, a series of peptides was synthesised with isosteric mutations. The interaction of the peptides with MN12H2 was analysed with a surface plasmon resonance competition assay yielding equilibrium binding constants in solution (K_S). The binding affinity seems to be largely determined by entropy, and the side chain of Asn¹⁸⁶ is sensitive for charge, inversion, hydrophobicity and size. Head-to-tail cyclisation of the peptide in a nine-amino-acid ring gives little reduction in affinity. It is concluded that the scoring function of LUDI does not help in optimisation of the peptide lead for MN12H2 binding. Other more elaborate molecular mechanics calculations show similar results. This implies that our current knowledge of molecular recognition is insufficient for explaining a case of peptide-protein binding, where the design process requires subtle changes in structure (from lead finding to lead optimisation).     

Insights into molecular interactions between CaM and its inhibitors from molecular dynamics simulations and experimental data

In order to contribute to the structural basis for rational design of calmodulin (CaM) inhibitors, we analyzed the interaction of CaM with 14 classic antagonists and two compounds that do not affect CaM, using docking and molecular dynamics (MD) simulations, and the data were compared to available experimental data. The Ca²⁺-CaM-Ligands complexes were simulated 20 ns, with CaM starting in the “open” and “closed” conformations. The analysis of the MD simulations provided insight into the conformational changes undergone by CaM during its interaction with these ligands. These simulations were used to predict the binding free energies (ΔG) from contributions ΔH and ΔS, giving useful information about CaM ligand binding thermodynamics. The ΔG predicted for the CaM’s inhibitors correlated well with available experimental data as the r² obtained was 0.76 and 0.82 for the group of xanthones. Additionally, valuable information is presented here: I) CaM has two preferred ligand binding sites in the open conformation known as site 1 and 4, II) CaM can bind ligands of diverse structural nature, III) the flexibility of CaM is reduced by the union of its ligands, leading to a reduction in the Ca²⁺-CaM entropy, IV) enthalpy dominates the molecular recognition process in the system Ca²⁺-CaM-Ligand, and V) the ligands making more extensive contact with the protein have higher affinity for Ca²⁺-CaM. Despite their limitations, docking and MD simulations in combination with experimental data continue to be excellent tools for research in pharmacology, toward a rational design of new drugs.     

Lipidated peptides derived from intracellular loops 2 and 3 of the urotensin II receptor act as biased allosteric ligands

Over the last decade, the urotensinergic system, composed of one G protein-coupled receptor and two endogenous ligands, has garnered significant attention as a promising new target for the treatment of various cardiovascular diseases. Indeed, this system is associated with various biomarkers of cardiovascular dysfunctions and is involved in changes in cardiac contractility, fibrosis, and hypertrophy contributing, like the angiotensinergic system, to the pathogenesis and progression of heart failure. Significant investment has been made toward the development of clinically relevant UT ligands for therapeutic intervention, but with little or no success to date. This system therefore remains to be therapeutically exploited. Pepducins and other lipidated peptides have been used as both mechanistic probes and potential therapeutics; therefore, pepducins derived from the human urotensin II receptor might represent unique tools to generate signaling bias and study hUT signaling networks. Two hUT-derived pepducins, derived from the second and the third intracellular loop of the receptor (hUT-Pep2 and [Trp¹, Leu²]hUT-Pep3, respectively), were synthesized and pharmacologically characterized. Our results demonstrated that hUT-Pep2 and [Trp¹, Leu²]hUT-Pep3 acted as biased ago-allosteric modulators, triggered ERK_1/2 phosphorylation and, to a lesser extent, IP₁ production, and stimulated cell proliferation yet were devoid of contractile activity. Interestingly, both hUT-derived pepducins were able to modulate human urotensin II (hUII)- and urotensin II-related peptide (URP)-mediated contraction albeit to different extents. These new derivatives represent unique tools to reveal the intricacies of hUT signaling and also a novel avenue for the design of allosteric ligands selectively targeting hUT signaling potentially.     

Highly flexible O,O′,N ligands and their Fe, Ni, Cu and Zn complexes

Three new chiral ligands bearing an O,O′,N donor set (O_methoxyO_hydroxyN_pyridine) were synthesised and coordinated to Fe^III, Fe^II, Ni^II, Cu^II and Zn^II to yield complexes with the general formula [M(OON)Cl_x]_y. While the pyridine N and the hydroxy O atoms coordinate strongly to all applied metal ions, the methoxy donor seems not to be involved in coordination, although some evidence for a weak interaction between O_Me and the Zn^II were found in NMR spectra. In the bidentate O′,N coordination mode the new ligands exhibit several coordination geometries as analysed in the solid compounds by XRD, EXAFS and EPR and in solution by UV-Vis absorption, cyclic voltammetry, EXAFS, EPR or NMR spectroscopy.     

Nickel and copper complexes with few amide-based macrocyclic and open-chain ligands

The present work shows three new amide-based ligands H₂L¹, H₂L² and H₂L³ and their nickel and copper complexes. The X-ray structural analysis substantiate that the ligands constitute a square-based basal plane around the metal center. The crystal structures also show interesting solid state packing due to hydrogen-bonding and various weak C?H interactions. The solution-based spectral studies support the solid-state geometry observed for these complexes. The electrochemical results show that the Ni^3+/2+ and Cu^3+/2+ redox couple primarily depends on the N₄ donors composed of N_amide and N_amine atoms. It was observed that the ligands H₂L¹ and H₂L² are better suited to stabilize the Cu(III) species whereas ligand H₂L³ is ideal for the stabilization of Ni(III) species. On the basis of electrochemical findings, transient Ni³⁺ species were generated and characterized by the absorption spectroscopy.     

Will combinatorial chemistry deliver real medicines?

Over the next decade, the impact of library synthesis will play a major role in shortening the lead optimization phase of drug discovery. The prognosis for combinatorial chemistry to discover fundamentally different new classes of therapeutically active small molecules against some of the more difficult biological targets is less certain. Expectations are high because the technology potentially allows us to sample available drug space by synthesizing all possible small molecule ligands (variously estimated to be between 10³⁰–10⁵⁰ compounds). Some caution is advised, however, since, despite recent increases in high-throughput screening of substantially greater numbers of synthetic compounds and natural products, we are not routinely finding a plethora of new structures. The outcome may be that combinatorial chemistry offers us the ability to work faster on finding ligands for well-established tractable targets, such as G-protein-coupled receptors, ion channels or proteases, rather than, say, the more complex protein—protein interactions which from the majority of targets in signal transduction pathways.     

New amino-dithiaphospholanes and phosphoramidodithioites and their rhodium and iridium complexes

New sulfur derivatives of phosphoramidite ligands were synthesized and the impact of the sulfur unit on the spectroscopic properties of their rhodium and iridium complexes was investigated. The new ligands Bn₂NPSCH₂CH₂S^a(P-S^a) (Bn = benzyl, 4), Bn₂NPSCHCHS^a(CH₂)₃C^aH₂(P-S^a)(C^a-S^a) (6) and Bn₂NP(4-XC₆H₄OMe)₂ (X = S, 7a; X = O, 7b) were converted to the rhodium and iridium complexes trans-[Rh(CO)Cl(L)₂] (L = 4, 6, 7), [RhCl(COD)(L)] (L = 4, 6, 7), [IrCl(COD)(7a)] and [IrCl₂Cp∗(6)]. For comparison, some phosphoramidite complexes of these formulations also were synthesized. The new metal complexes were spectroscopically analyzed. For the carbonyl complexes, the ν_CO IR stretching frequencies were lower than for the corresponding phosphite and phosphoramidite ligands. The ¹J_PRh coupling constants for the rhodium complexes with the new ligands were also smaller than for the respective phosphoramidite and phosphite complexes. Finally, the ¹J_PSe coupling constants of the selenides of the new ligands were lower than those of the phosphoramidite ligands but higher than for PPh₃. The spectroscopic data reveal that the new thio ligands 4, 6 and 7a are more electron donating than phosphites and phosphoramidites but less electron donating than PPh₃.     

Fast screening and structural elucidation of G-quadruplex ligands from a mixture via G-quadruplex recognition and NMR methods

Currently, there is a considerable interest in discovering G-quadruplex ligands. Plant-derived agents, because of their diversity in structure and bioactivity and low toxicity, may be a very diverse source of G-quadruplex ligands. However, up to now, the screening of G-quadruplex ligands from natural plant extract has not been reported. Herein, in order to develop a simple method for fast identifying G-quadruplex ligands from plant extract, we intended to substitute the spectral shift in the imino region (δ 10–12) in ¹H NMR spectra of G-quadruplex for in vitro bioassay to judge the existence/nonexistence of G-quadruplex ligand(s) in plant extract, and then couple G-quadruplex recognition with NMR based structure elucidation to identify the structure of the ligand(s) without the need of prior separation. In this paper, we successfully screened a G-quadruplex ligand from a simulated plant extract using this approach. This research work provides a promising tactic to find new leading compounds from nature plant extract.     

Two new bulky amido ligands useful for the preparation of metal complexes and examples of their reactivity

The search for new ligands with interesting properties is a quest that can occupy much of a synthetic chemist’s time. We have recently discovered two new ligands based on an adamantyl-substituted, 2,6-ⁱPr₂-substituted phenyl (Dipp) system. In an attempt to prepare the extremely bulky amine [(ad)(2,6-ⁱPr₂C₆H₃)NH] (ad = adamantyl) we found instead that the adamantyl group attacks the aromatic ring in the 4-position to form a new primary amine, (4-ad-2,6-ⁱPr₂C₆H₂)NH₂ (1) (ad-Dipp-NH₂), characterized by normal techniques. Compound 1 could be converted into a Li salt by a 1:1 reaction with ⁿBuLi, or converted into a more bulky silylamine, [(ad-Dipp)NH(SiMe₃)] (3), by treatment with Me₃SiCl. We have characterized the lithium salt by X-ray crystallography as the dimeric complex, [(ad-Dipp)NHLi(Et₂O)]₂ (2). The lithium amide can be used as a reagent towards metal halides, and we have discovered that its reaction with SnCl₂ yields a compound with a tetrameric, [Sn-N]₄ cubane-like cage structure. We have also demonstrated the ligand behavior of 3 by its reaction with Bu₂Mg in THF to form a monomeric Mg-amide with two THF solvent molecules attached. These new ligands can provide advantages over conventional ligands in terms of improved solubility and ease of crystallization.     

Penta- and heteropentadienyl ligands coordinated to beryllium

In this work we have performed a systematic study of new organometallic complexes containing penta- and heteropentadienyl (CH₂CHCHCHX, X?=?CH₂, O, NH, S) ligands coordinated to beryllium. Calculated complexes were studied using the density functional theory (PBE) in combination with the 6-311++G(3d,2p) basis set. The coordination number on the beryllium atom varies according to the type of ligand. Pentadienyl ligand shows hapticities η¹ and η⁵, while heteropentadienyl ligands display η¹ and η² hapticities. A Wiberg bond indices study was performed in order to get information about their bond orders.

In Vitro Evaluation of 11C-Labeled (S)-Nicotine, (S)-3-Methyl-5-(1-Methyl-2-Pyrrolidinyl)isoxazole, and (R,S)-1-Methyl-2-(3-Pyridyl)azetidine as Nicotinic Receptor Ligands for Positron Emission Tomography Studies

Abstract: The binding characteristics of the novel ¹¹C-labeled nicotinic ligands (R,S)-1-methyl-2-(3-pyridyl) azetidine (MPA) and (S)-3-methyl-5-(1-methyl-2-pyrrolidinyl)isoxazole (ABT-418) were investigated in comparison with those of (S)-[¹¹C]nicotine in vitro in the rat brain to be able to predict the binding properties of the new ligands for positron emission tomography studies in vivo. The data from time-resolved experiments for all ligands indicated fast binding kinetics, with the exception of a slower dissociation of [¹¹C]MPA in comparison with (S)-[¹¹C]nicotine and [¹¹C]ABT-418. Saturation experiments revealed for all ligands two nicotinic receptor binding sites with affinity constants (K_D values) of 2.4 and 560 nM and binding site densities (B_max values) of 65.5 and 223 fmol/mg of protein for (S)-[¹¹C]nicotine, K_D values of 0.011 and 2.2 nM and B_max values of 4.4 and 70.7 fmol/mg of protein for [¹¹C]MPA, and K_D values of 1.3 and 33.4 nM and B_max values of 8.8 and 69.2 fmol/mg of protein for [¹¹C]ABT-418. In competing with the ¹¹C-ligands, epibatidine was most potent, followed by cytisine. A different rank order of potencies was found for (?)-nicotine, (+)-nicotine, MPA, and ABT-418 displacing each of the ¹¹C-ligands. Autoradiograms displayed a similar pattern of receptor binding for all ligands, whereby [¹¹C]MPA showed the most distinct binding pattern and the lowest nonspecific binding. We conclude that the three ¹¹C-labeled nicotinic ligands were suitable for characterizing nicotinic receptors in vitro. The very high affinity of [¹¹C]MPA to nicotinic acetylcholine receptors, its low nonspecific binding, and especially the slower dissociation kinetics of the [¹¹C]MPA from the putative high-affinity nicotinic acetylcholine receptor binding site compared with (S)-[¹¹C]nicotine and [¹¹C]ABT-418 raise the level of interest in [¹¹C]MPA for application in positron emission tomography.     

A Computer-Aided Radiopharmaceutical Drug Design Study Using Ab Initio and Molecular Mechanics Methods

This is an investigation of technetium ligands and their complexes with [TcO]³⁺ using ab initio population analysis and molecular mechanics conformational searching methods. Calculated atomic electronic populations on the technetium atom in complexes with a number of ligands gauge the degree of covalent bonding between technetium and these ligands. Here a reduction in the positive charge on the [TcO]³⁺ moiety by complexation with a given ligand is correlated with covalent bonding. Our ab initio results suggest that ligands with more sulphur atoms have better covalent bonding to technetium than do other ligands. A conformational analysis of the uncomplexed ligands indicates that conformational reorganization before complexation correlates inversely with stable complex formation. This conformational analysis shows that ligands with ethylene carbonyl bridges have low energy conformations closer to the final complexation geometries than do ligands with ethylene, propylene or propylene carbonyl bridges. The presence of these low energy conformations facilitates a faster complexation of the ethylene carbonyl [TcO]³⁺ moiety. This result produces a kinetic explaination why ethylene carbonyl bridged ligands form stable complexes while many other ligands do not [1]. The conclusion is that kinetic and thermodynamic considerations play a role in stable complex formation between these ligands and technetium.     

Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

Divalent Mg²⁺ ions often serve as cofactors in enzyme or ribozyme-catalyzed phosphoryl transfer reactions. In this work, the interaction of Mg²⁺ ions and di-metal bridge complexes with phosphates, phosphoranes, and other biological ligands relevant to RNA catalysis are characterized with density functional methods. The effect of bulk solvent is treated with two continuum solvation methods (PCM and COSMO) for comparison. The relative binding affinity for different biological ligands to Mg²⁺ are quantified in different protonation states. The structure and stability of the single-metal and di-metal complexes are characterized, and the changes in phosphate and phosphorane geometry induced by metal ion binding are discussed. Di-metal bridge complexes are a ubiquitous motif and the key factors governing their electrostatic stabilization are outlined. The results presented here provide quantitative characterization of metal ion binding to ligands of importance to RNA catalysis, and lay the groundwork for design of new generation quantum models that can be applied to the full biological enzymatic systems.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0583-7An erratum to this article can be found at